Chromatin-associated RNAs have important regulatory functions and can promote the formation of spatial compartments in the nucleus. But their conjugated genomic loci and numerous roles in the genome remain largely unknown. Further, we described an efficient method for mapping site-specific chromatin-associated RNA–DNA interactions followed by paired-end-tag sequencing (ChRD-PET), based on chromatin immunoprecipitation and RNA–DNA proximity ligation. A pipeline was also developed for ChRD-PET data analysis and get high-confident RNA–DNA interactions.